SAXSdb — 1rjp

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1. Protein Identity and Related Structures Protein Identity & Related Structures

D-aminoacylase

Alcaligenes faecalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ACETATE ION × 2 ZINC ION × 1 COPPER (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9AGH8_ALCFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–496； UniProt 1–484

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1rjp
Deposition date deposition_date	2003-11-20
Structure title title	Crystal structure of D-aminoacylase in complex with 100mM CuCl2
Keywords keywords	TIM barrel, beta barrel, insertion, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1rjp__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1rjp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rjp__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	22.67 Å
Rg (electron density)	21.61 Å
Total Rg	22.41 Å
Atom count	3599
Residues	474
Excluded volume	63643 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rjp__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	D-aminoacylase
Molecular weight formula_weight	53466.2 kDa
EC 编号 ec_number	3.5.1.81
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3823

MRGSHHHHHHGSMSQPDATPFDYILSGGTVIDGTNAPGRLADVGVRGDRIAAVGDLSASSARRRIDVAGKVVSPGFIDSHTHDDNYLLKHRDMTPKISQGVTTVVTGNCGISLAPLAHANPPAPLDLLDEGGSFRFARFSDYLEALRAAPPAVNAACMVGHSTLRAAVMPDLRREATADEIQAMQALADDALASGAIGISTGAFYPPAAHASTEEIIEVCRPLITHGGVYATHMRDEGEHIVQALEETFRIGRELDVPVVISHHKVMGKLNFGRSKETLALIEAAMASQDVSLDAYPYVAGSTMLKQDRVLLAGRTLITWCKPYPELSGRDLEEIAAERGKSKYDVVPELQPAGAIYFMMDEPDVQRILAFGPTMIGSDGLPHDERPHPRLWGTFPRVLGHYSRDLGLFPLETAVWKMTGLTAAKFGLAERGQVQPGYYADLVVFDPATVADSATFEHPTERAAGIHSVYVNGAAVWEDQSFTGQHAGRVLNRAGA

Source Source

Source organism organism	Alcaligenes faecalis
NCBI taxonomy ID ncbi_taxonomy_id	511
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1rjpa1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.6 — D-aminoacylase

Domain ID domain_id	d1rjpa2
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.6 — D-aminoacylase

Domain ID domain_id	d1rjpa3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.11 — D-aminoacylase, catalytic domain

CATH v4.4 (3 domains)

Domain ID domain_id	1rjpA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	1rjpA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	1rjpA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	130 — D-aminoacylase. Domain 3

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Unit-cell length a length_a	60.343 Å
Unit-cell length b length_b	77.099 Å
Unit-cell length c length_c	135.891 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	28.100 Å
R factor r_factor	—
R_work r_work	0.1860
R_free r_free	0.2160

Crystal structure of D-aminoacylase in complex with 100mM CuCl2

1. Protein Identity and Related Structures Protein Identity & Related Structures

D-aminoacylase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1rjp__assembly_1__model_1

1rjp__assembly_1__model_1 | I(q)

1rjp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (3)

Crystal structure of D-aminoacylase in complex with 100mM CuCl2

1. Protein Identity and Related Structures Protein Identity & Related Structures

D-aminoacylase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1rjp__assembly_1__model_1

1rjp__assembly_1__model_1 | I(q)

1rjp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (3)